Thanks very much for that.
pihole.log: https://tricorder.pi-hole.net/avj5ykmijh
pihole-FTL.log: https://tricorder.pi-hole.net/e9ynwc2sl3
Just registered to chime in here also. I am having the same issue on a Pi2b, and on a Pi4 (different networks). When I disable for any length of time, DNS completely breaks and I need to restart the Pi.
We merged this fix into the code for Pi-hole v5.1
It should resolve these issues.
Thanks - That is good to hear. When is 5.1 being released?
Soon (TM)
I just saw this happen with 5.1.1. 
I disabled pihole for 30 seconds, and DNS didn't resolve any domains for at least a minute.
During this time:
pi@pihole:~ $ pihole status
[✓] DNS service is running
[✗] Pi-hole blocking is Disabled
pihole restartdns reload didn't resolve the problem.
pihole.log: https://tricorder.pi-hole.net/go3izzfe6t
pihole-FTL.log: https://tricorder.pi-hole.net/jden0vxm0i
Your
pihole-FTL.log:[2020-07-22 06:45:45.524 1511M] Reloading DNS cache [2020-07-22 07:27:11.748 1511M] Blocking status is disabled [2020-07-22 07:27:43.357 1511M] INFO: No regex whitelist entries found [2020-07-22 07:27:43.568 1511M] Compiled 0 whitelist and 1 blacklist regex filters for 78 clients in 215.3 msec [2020-07-22 07:28:13.822 1511M] Reloading DNS cache [2020-07-22 07:28:13.822 1511M] Blocking status is enabled [2020-07-22 07:28:42.839 1511M] INFO: No regex whitelist entries found [2020-07-22 07:28:43.049 1511M] Compiled 0 whitelist and 1 blacklist regex filters for 78 clients in 214.8 msec [2020-07-22 07:29:16.632 1511M] Reloading DNS cache [2020-07-22 07:29:16.633 1511M] Blocking status is enabled
I wonder if this comes from the large number of clients. Does 78 sound reasonable to you?
If you also have a very large number of domains, this may end up in FTL having to purge a lot of memory and, somehow, it takes too long for this (N * M problem). What is the average number of queries per day in your network and what hardware are you running your Pi-hole on?
I just checked my router's device list and 78 is accurate, though it's closer to 50 at any given moment as devices go to sleep, etc. That supports four people and several devices running all day. Smart TVs, wifi scales, doorbell, cameras, phones, tablets, e-readers, smart speakers, computers, etc.
Here's the queries from the 24 hour period yesterday. It sort of peaked around 1100, but averages mainly hover around 500-600 on any given day.
I'm running PiHole on a Raspberry Pi Zero W. I agree that it could be the weak link in the chain here, but it did run PiHole 4.x without a hiccup for years.
Yeah, i see that, however Pi-hole v5.0 introduced per-client filtering effectively making everything cost roughly
N(client) * (amount of work with v4.x treating blocking the same for every client)
In reality, it is somewhat less dramatic, however, it can explain why you are now seeing 30 seconds of delay where there was maybe 1-2 before (which went unnoticed).
I don't know if we can do much about it, but I will think about it some more.
For comparison: I have 5 devices in my home network with 2 people actively using the web. But setups differ 
Please send us a fresh debug token.
You got it: https://tricorder.pi-hole.net/217y6hubyn
And thanks @DL6ER for the context on how the new filtering style works. I remember seeing some messaging that suggested that weaker devices like the Zero W wouldn't be supported anymore during the 5.0 beta, but that all went away with the 5.0 release. Might need to revisit that decision. And it's all my fault! 
I think there was some confusion happening here. The bugfix for this was not merged into v5.1.1 at the time you posted. It was still open for review. They just merged it an hour ago. Please update and try again. Maybe this can safe your Pi Zero from scrapping.
Good lookin' out, but pihole -up yields nothing.
I think I need to wait for the next official point release.
In the meantime I'm investigating rolling back to 4.x somehow. I haven't really been able to pause PiHole on 5.x.
Please try
pihole checkout ftl release/v5.2
to get the latest FTL code. This will hopefully eliminate the delays.
Just dropping in to say FTL 5.2 has (apparently!) fixed this for me.
I'm now able to pause Pihole on my Pi Zero W without losing DNS across my network.
Thank you to the Pi-hole team for whatever re-engineering was necessary to make this happen. I'm sure I speak for all low-power pihole device users
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